Last updated: 2023-05-26

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Knit directory: LungCancer_SotilloLab/analysis/

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Section 1: Data input and preprocessing

This is the part where the Spetronaut output data were processed and cleaned by SmartPhos package.

Section 2: Exploratory data analysis and quality check

In this part, exploratory data analyses, such as PCA and clustering were performed to get an overview of the data structure and data quality.

Section 3: Differential expression analysis on protein level

In this analysis, the differential expression on protein level was analyzed. Differential expression was performed for each drug versus DMSO and other drugs. In the report, only time point 0.17h and 16h were shown. At the end of the report, the full differential expression analysis results (all comparisons and time points) as well as processed protein expression matrix can be downloaded.

Section 4: Differential expression analysis on phosphorylation level

The same analysis as Section 3, but for phosphorylation sites.

Section 5: Differential expression analysis on phosphorylation level normalized by protein expression

The same analysis as Section 3 and 4, but on the phosphorylation normalized by protein expression. Basically on the ratio between phosphorylation intensity and protein intensity. This can avoid phosphorylation changes that only caused by protein expression change.

Section 6: Explore Dasatinib off-target effect

In this analysis, the protein expression and phosphorylation intensity of a list of potential Dasatinib down-stream targets were plotted. Only visualization. No hypothesis testing was involved.

Section 7: Kinase pathway analysis

In this part, I used a tool called kinasePA (https://pubmed.ncbi.nlm.nih.gov/27145998/), to summarise the kinase activity changes upon drug treatment.

Section 8: Network visualization

In this analysis, I tried to visualize the relationship between the kinases and their targets that were differentially expressed after drug treatments.

Section 9: Analysis of the V1 V3 mTDCs proteomic data

The mTDCs DDA proteomic data was analyzed in this part. The results can be used for Figure 1 and Figure 5G in the manuscript.

Section 10: Kinase activity analysis for the manuscript

The figures in this report can be used for figure 6A and supplementary figures.